BN1827 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 3.4120e-06 5.8901e-04
Layer 5 4.1763e-05 4.4310e-04
Layer 6 1.6332e-04 2.6675e-03
Layer 3 7.2311e-04 4.1854e-02
Layer 1 1.5390e-03 1.2622e-01
Layer 2 1.7871e-03 9.4436e-02
WM 9.9927e-01 5.5477e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
ATP6V0C Expression Distribution
Gene Specificity Score (GSS)
ATP6V0C GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
ATP6V0C Layer 5 2.4668 0.7435
STMN1 Layer 4 2.6895 0.7417
YWHAG Layer 5 2.8281 0.7417
MTCH1 Layer 5 2.6602 0.7406
ATP6V0A1 Layer 5 2.7041 0.7406
SNAP91 Layer 4 2.4883 0.7392
TUBB2A Layer 5 2.7793 0.7368
ENO2 Layer 5 2.7793 0.7359
SYT1 Layer 5 2.6895 0.7321
PRKAR1B Layer 5 2.7070 0.7315
DNM1 Layer 5 2.8906 0.7313
TPI1 Layer 5 2.6719 0.7296
KLC1 Layer 5 2.7480 0.7292
ARL6IP1 Layer 5 2.7656 0.7284
FAIM2 Layer 4 2.6484 0.7271
RTN3 Layer 5 2.6660 0.7240
RNF11 Layer 5 2.7969 0.7237
YWHAZ Layer 5 2.5781 0.7226
GDI1 Layer 5 2.5898 0.7221
MORF4L1 Layer 5 2.7305 0.7221
SNRPN Layer 5 2.7246 0.7219
VAMP2 Layer 5 2.6895 0.7212
ARF1 Layer 5 2.4609 0.7205
MAPK8IP2 Layer 5 2.5508 0.7191
NAPB Layer 5 2.9697 0.7188
SYN1 Layer 5 2.6367 0.7184
STMN2 Layer 5 3.2363 0.7181
DPYSL2 Layer 4 2.3750 0.7174
NCDN Layer 4 2.6836 0.7144
EEF1A2 Layer 5 2.9727 0.7133
CLSTN1 Layer 5 2.4570 0.7120
RAB6B Layer 5 2.7041 0.7118
BSCL2 Layer 5 2.6367 0.7117
RTN1 Layer 5 2.6602 0.7107
CALM3 Layer 5 2.5605 0.7107
SYP Layer 5 2.6836 0.7103
ANK2 Layer 5 2.6836 0.7095
FXYD6 Layer 5 2.8906 0.7089
SYN2 Layer 5 3.2500 0.7085
NORAD Layer 5 2.5273 0.7084
TOLLIP Layer 5 2.5664 0.7077
ATP1B1 Layer 5 2.6016 0.7066
UCHL1 Layer 5 2.5566 0.7061
GRIN1 Layer 4 2.6719 0.7061
EEF2 Layer 5 2.3027 0.7058
VSNL1 Layer 5 2.7422 0.7055
SPTAN1 Layer 5 2.5273 0.7054
SNCA Layer 5 2.6426 0.7028
THY1 Layer 5 2.6777 0.7027
WBP2 Layer 5 2.4785 0.7018

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1827
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1827_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1827/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1827/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1827/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1827/report/PD/BN1827_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1827/report/PD/BN1827_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:05:33
  • Number of Processes: 10
  • Spending Time: 0h 3m